The invention provides a spacecraft module flexible docking mechanism, belongs to the technical field of spacecraft docking, and specifically relates to a spacecraft module flexible docking mechanism.The problems that the existing rigid conical rod type docking mechanism is complicated in structure, a special energy absorbing mechanism is required, disturbance to the stars is great are solved, and the problems of low connection rigidity and large jitter of the existing flexible conical rod type docking mechanism are solved. The spacecraft module flexible docking mechanism comprises an activeend docking module and a passive end docking module,the active end docking module comprises a guiding head, a flexible rod, a separating component, a connecting and unlocking component, and a drivingcomponent, and the passive end docking module comprises a guiding cone, a bearing section, and a passive end flange.The spacecraft module flexible docking mechanism is mainly used for space docking tasks with spacecraftswhich are sensitive to impact and require precise operation with the aid of autonomous power or robotic arms.